Water in 12 Volt Battery Compartment...Unrelated to Horrible Smell?

OK, I've been reading a lot about this problem occurring in the pre 2010 prius where there is a crack around the hatch that fills the 12V battery well with water. About a month ago, I started getting a whiff of something rotting. A mix of the dead smell and rotting fruit. I was certain one of my kids left some food in the car or something got in the HVAC vent. As time has gone by, the odor has changed to more of a rotting leaves kind of smell.

I got out my shopvac and a snake camera. I went through the HVAC system and found that the filter was pulled back a bit. I replaced it on the spot. I found a few leaves and dust and that was it. The air coming from the vents from the outside smells clean. There were lots of wet leaves in the engine bay, but it wasn't the problem.

I started tearing apart the trunk because sometimes stuff spills into the tire well. I found the spare tire had turned brown on the tread.

I opened the battery compartment and found about an inch of standing milky white water. The kicker here is that the water didn't seem to smell that bad! I dried it all up and bleached the metal to kill any mold that might be in the residue...but the odor remains. The car smells awful!

I have torn apart the back of the car but I cannot find the source of the leak. I actually think it was from the car wash or going through a puddle and water got in the rear vent. The battery fender vent vanes were flapping with gusts of wind today, but even after a heavy rainstorm no new water has gotten in.

The car was hit in the parking lot and the rear fender moved about an 1/8th of an inch from the bumper, but there are no obvious signs of water entry anywhere... in fact, I was even suspicious that it might have come from the battery itself, but I didn't touch it (used paper towels on a snake to dry it up under there). I didn't think to try baking soda to see if it was an acid, which makes bleach pretty stupid to use...but I didn't see any foaming.


TL;DR Found water in my 12V battery compartment. My car smells like nice person. Cleaning out water did not improve smell. Nothing in HVAC system, it is only clean air source in car. No signs of water ingress above 12v battery well. After rainstorm, no additional water found in battery well. Fender vent flaps in gusty wind, but still no new water.

Any ideas here? I am at a loss as to where else to look for bad smells. Do I need to try to look under the hybrid battery too? I theorize that the liquid either came from the battery itself or from crossing a flooded road a year ago. (it was only deep enough to lap against plastic undercarriage at front bumper)

 

Found it! I don't know how I missed it. There was water damage inside the fender liner. Pic 1
I traced it to the tailight. The nuts were loose and the foam rubber seals were ruined. Crazy for a 6 yr old car! A pile of leaves and muck had accumulated and was directing water inside the car. There is another storm on the way, so I had to do a quick fix and used RTV silixone to make a temporary gasket.
Thanks for the input all.